The human immunodeficiency virus (HIV), as its name suggest, is characterized by progressive immunologic deterioration which over a period of time results in neurologic disorders and opportunistic infections leading to acquired immunodeficiency syndrome (AIDS). The search to find antiretroviral therapy for treatment of the 34 million people globally infected with Human Immunodeficiency Virus (HIV) is an ongoing one. Although there are over 20 antiretroviral drugs approved for the treatment of HIV that will halt replication of the virus, the complete eradication of this fatal disease remains a scientific challenge. Drug resistance, tolerability and HIV latency are major factors contributing to ART failure and ultimately success in finding a cure.2-4 Hence, there remains a critical and unmet need to identify novel antiretroviral drug candidates active against HIV-1 resistant mutations for treatment of HIV-1 infection.
Integrase is one of the essential enzymes required for replication of HIV and is encoded by viral pol gene. Integration of virally transcribed cDNA into host DNA is an essential step for viral replication and the continuation of HIV life cycle. Upon synthesis of viral DNA in the cytoplasm of the cell, a series of interactions of viral proteins, matrix protein, a triple stranded cDNA flap and cellular cofactors, with integrase (IN) forms the pre-integration complex (PIC). Transport of viral DNA to the nucleus of the cell requires the formation of PIC which binds nuclear transport receptors via a nuclear localization signal (NLS) thereby allowing for entry into the nucleus where viral cDNA will integrate into host DNA. Successful integration of viral cDNA into host DNA is an essential step for viral replication and the continuation of HIV life cycle hence, IN is considered a good drug target for the development of ARV drugs.
There are multiple classes of antiretroviral (ARV) drugs that target various stages of the HIV life cycle which elicit unique mechanisms of action. As the mechanism of action of integrase (IN) and the evolution of IN resistant mutations is swiftly unfolding, IN represents an untapped source of undiscovered ARV drugs. The success rate for discovery and development of integrase inhibitors is quite low with only two IN inhibitors currently on the market, Raltegravir (RAL) developed by Merck & Co and Elvitegravir (EVG), as a combination therapy, developed by Gilead Science. Both drugs binds the catalytic site of IN located in the catalytic core domain and function by inhibiting the strand transfer process of vDNA into host DNA hence are referred to as integrase strand transfer inhibitors (INSTI). However due to the increasing clinical reports of INSTI resistance there is a need to design new class of IN inhibitors with novel mechanism of action. Specifically RAL and EVG exhibit consistant resistant pathways Q148HRQ/G140S and N155H/E92Q. A more recent approach to targeting IN is with small molecule inhibitors of LEDGF/p75 known as LEDGINs. Integrase inhibitors have been classified into five categories: (1) DNA-binding inhibitors, (2) 3′ processing inhibitors, (3) nuclear translocation/import inhibitors, (4) strand transfer inhibitors, and (5) gap repair inhibitors. Currently there are no reports of small molecule inhibitors that target allosteric site on CTD of IN.
The structure of IN plays a major role in dictating its function hence, complete elucidation of its structure will contribute significantly to the discovery of integrase inhibitors. To date the complete crystal structure of IN has not been elucidated, however we do know IN comprises 288 amino and has three domains, N-terminal domain (NTD), catalytic core domain (CCD) and the C-terminal domain (CTD). Each IN monomer will combine to form a tetrameric IN structure. The NTD and CCD have conserved and functional motifs, while the CTD is the least conserved of the three. The conserved region of the NTD (residues 1-50) contains a sequence of HHCC residues that form a zinc finger motif which functions to chelate one zinc atom per IN monomer. In the absence of zinc the NTD of IN is destabilized and become disordered and formation of the multimeric form of IN is not achieved and could disrupt its activity.22 The CCD (residues 51-212) conserved region comprises a triad of acidic residue that form the DDE motif It is essential for 3′ processing and strand transfer processes. Integrase has nuclease activity that is site specific for cleaving two nucleosides at the 3′ end of viral DNA, a process known as 3′ processing. Subsequently, the strand transfer process ensues and it involves the 3 ends of viral DNA inserting into host DNA. The CTD (residues 213-288) on the other hand, is less conserved and is essential for IN-IN and non-specific IN-DNA (residues 220-270) interactions.